If you have your original files, you can re-send them all to Amazon for conversion. Many people delete the originals once they have the Kindle version, so this option won't work for everyone. So, here's what you can do:
1. You will need to install MobiPerl <https://dev.mobileread.com/trac/mobiperl>
2. You will need to install Mobi2Mobi_GUI <http://wiki.mobileread.com/wiki/Kindle_Mobi2Mobi_GUI_Vista/XP>
3. Use Mobi2Mobi_GUI to change the cdetype to PDOC
Note: cdetype is found in the EXTH type drop-down box (don't forget to check the box next to any field you're changing)
4. Click "convert"
Your new file will now show up in the Personal Docs filter on Kindle 2.
Now, there should be a way to change this from the mobi2mobi command line. I know it can change mobiheader items, even though the switches aren't undocumented, but I can't figure out how to change the extended header fields. Below is the item that tells Kindle 2 that the file is a personal document:
EXTH item: 501 - CDEContentType - 4 - PDOC
I'd love to have comments on command line (or Mac-friendly) methods.